Empty `.xlsx` file

[hariszaf]

Hi!

I tried to run the tutorial_atomicallyResolveReconstruction.mlx tutorial on MATLAB online and I got the following error:

Error using readtable (line 498)
Unable to open file '/MATLAB Drive/COBRA/fork-cobratoolbox/tutorials/analysis/atomicallyResolveReconstruction/metaboliteIds.xlsx as a workbook. Check that file exists, read access is available, and the file is a valid spreadsheet file. 

Error in addMetInfoInCBmodel (line 31)
   dbData = readtable(inputData);

Then I cheched for the file COBRA.tutorials/analysis/atomicallyResolveReconstruction/metaboliteIds.xlsx and I realised that is an empty one.

Should that be this way?

Apologies if I missed something on the way.

Regards, Haris

[rmtfleming]

Hi Haris, initCobraToolbox again then it should be there as an .xlxs_tmp file now. Regards, Ronan

On Wed, 6 Oct 2021 at 08:10, hariszaf @.***> wrote:

Hi!

I tried to run the tutorial_atomicallyResolveReconstruction.mlx tutorial on MATLAB online and I got the following error:

Error using readtable (line 498) Unable to open file '/MATLAB Drive/COBRA/fork-cobratoolbox/tutorials/analysis/atomicallyResolveReconstruction/metaboliteIds.xlsx as a workbook. Check that file exists, read access is available, and the file is a valid spreadsheet file.

Error in addMetInfoInCBmodel (line 31) dbData = readtable(inputData);

Then I cheched for the file COBRA.tutorials/analysis/atomicallyResolveReconstruction/metaboliteIds.xlsx https://github.com/opencobra/COBRA.tutorials/blob/master/analysis/atomicallyResolveReconstruction/metaboliteIds.xlsx and I realised that is an empty one.

Should that be this way?

Apologies if I missed something on the way.

Regards, Haris

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--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

[hariszaf]

I tried to clone the cobratoolbox repo from scratch after your changes, however, when i ran

git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox

all submodules directories, i,e /binary, papers and /tutorials were empty.

I then ran

git submodule update --init

from inside /cobratoolbox and even i got the submodules, I was not able to run the tutorial_atomicallyResolveReconstruction.mlx tutorial. It seems that now you are using iDopaNeuro1 as your model - I am mentioning this to cross check I go the right commit.

Turorial tutorial_initConservedMoietyPaths was completed.

The tutorial_initConservedMoietyPaths however, returned the following error :

tutorial_initConservedMoietyPaths
Undefined function or variable `tutorial_initConservedMoietyPaths`

I also tried to run the initCobraToolbox command, as you mentioned, on MATLAB online but I got the initial error mentioned.
Is there any chance that you have the previous commit fixed in what we use in MATLAB online?

Appologies if I have not get something right. Haris

[rmtfleming]

Try running initCobraToolbox in matlab then see if it is working.

On Thu, 7 Oct 2021 at 01:38, hariszaf @.***> wrote:

I tried to clone the cobratoolbox repo from scratch after your changes, however, when i ran

git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox

all submodules directories, i,e /binary, papers and /tutorials were empty.

I then ran

git submodule update --init

from inside /cobratoolbox and even i got the submodules, I was not able to run the tutorial_atomicallyResolveReconstruction.mlx tutorial. It seems that now you are using iDopaNeuro1 as your model - I am mentioning this to cross check I go the right commit.

Turorial tutorial_initConservedMoietyPaths was completed.

The tutorial_initConservedMoietyPaths however, returned the following error :

tutorial_initConservedMoietyPaths Undefined function or variable tutorial_initConservedMoietyPaths

I also tried to run the initCobraToolbox command, as you mentioned, on MATLAB online but I got the initial error mentioned. Is there any chance that you have the previous commit fixed in what we use in MATLAB online?

Appologies if I have not get something right. Haris

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/opencobra/COBRA.tutorials/issues/155#issuecomment-937349712, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOUGRDWTID6XW7NRIETUFTTY7ANCNFSM5FNWQ64A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)